Bioconductor Cuffdiff

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3.9k

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dexseq bitseq cuffdiff Differential exon usage isoforms

9.8 years ago • updated 9.7 years ago elle ▴ 10

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3.7k

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RNA-seq / XLOC cuffdiff

updated 3.2 years ago by Lan • 0 • written 4.8 years ago by mg.mahabad1365 • 0

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1.8k

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WGCNA cuffdiff

6.5 years ago sbbinfo90 • 0

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2.3k

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SpliceR Cuffdiff

updated 9.5 years ago by deppt002 • 0 • written 9.8 years ago by mfahim • 0

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3.9k

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htseqtools deseq2 counts cuffdiff

9.1 years ago Jon Bråte ▴ 260

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1.9k

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cummeRbund Script analysis RNAseq cuffdiff

updated 9.9 years ago by andrew.j.skelton73 ▴ 370 • written 9.9 years ago by mfahim • 0

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1.9k

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deseq2 cuffdiff

updated 9.8 years ago by Michael Love 43k • written 9.8 years ago by a.de-giorgio12 • 0

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1.6k

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deseq2 cuffdiff differential gene expression

9.7 years ago Assa Yeroslaviz ★ 1.5k

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1.7k

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GAGE Cuffdiff gene names

updated 9.3 years ago by Luo Weijun ★ 1.6k • written 9.3 years ago by user31888 ▴ 30

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1.5k

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cuffdiff sqlite

7.3 years ago handgabriel • 0

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1.5k

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kegg readcufflinks cuffdiff cuff

updated 7.3 years ago by thokall ▴ 160 • written 7.3 years ago by pierre.biojoux • 0

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531

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cummeRbund cufflink cuffdiff

updated 19 months ago by James W. MacDonald 68k • written 20 months ago by sumitra • 0

12 results • Page 1 of 1

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Comment: DiffBind custom normalization factor by Abbie • 0

Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k

All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…

Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…

Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…

Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k

I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …

Votes

A: Machine learning in R book

Data preparation and Machine learning on time course RNAseq data

Answer: Use of org.Rn.eg.db with GRCr8 reference genome

A: use tximport's countsFromAbundance when using DESeq2

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